rs525028

Variant names:

• chr11-116834800-G-A
• rs525028

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.505 in 151,862 control chromosomes in the GnomAD database, including 23,112 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (23112 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76698 AN: 151744 Hom.: 23122 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.528

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.505 AC: 76686 AN: 151862 Hom.: 23112 Cov.: 30 AF XY: 0.497 AC XY: 36876 AN XY: 74202

African (AFR) AF: 0.193 AC: 7976 AN: 41430

American (AMR) AF: 0.502 AC: 7660 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2248 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1369 AN: 5126

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4812

European-Finnish (FIN) AF: 0.620 AC: 6533 AN: 10534

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46953 AN: 67942

Other (OTH) AF: 0.522 AC: 1095 AN: 2098

Alfa AF: 0.478 Hom.: 11602

Bravo AF: 0.485

Asia WGS AF: 0.303 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.48
PhyloP100		-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs525028; hg19: chr11-116705516;